Approximating persistence in a general class of population processes

We provide a general framework for estimating persistence in populations which may be affected by catastrophic events, and which are either unbounded or have very large ceilings. We model the population using a birth-death process modified to allow for downward jumps of arbitrary size. For such processes, it is typically necessary to truncate the process in order to make the evaluation of expected extinction times (and higher-order moments) computationally feasible. Hence, we give particular attention to the selection of a cut-off point at which to truncate the process, and we present a simple method for obtaining quantitative indicators of the suitability of a chosen cut-off. (c) 2005 Elsevier Inc. All rights reserved.

Modeling diffraction and imaging of laser beams by the mode-expansion method

We present a new method of modeling imaging of laser beams in the presence of diffraction. Our method is based on the concept of first orthogonally expanding the resultant diffraction field (that would have otherwise been obtained by the laborious application of the Huygens diffraction principle) and then representing it by an effective multimodal laser beam with different beam parameters. We show not only that the process of obtaining the new beam parameters is straightforward but also that it permits a different interpretation of the diffraction-caused focal shift in laser beams. All of the criteria that we have used to determine the minimum number of higher-order modes needed to accurately represent the diffraction field show that the mode-expansion method is numerically efficient. Finally, the characteristics of the mode-expansion method are such that it allows modeling of a vast array of diffraction problems, regardless of the characteristics of the incident laser beam, the diffracting element, or the observation plane. (C) 2005 Optical Society of America.

Brain maps, great and small: lessons from comparative studies of primate visual cortical organization

In this paper, we review evidence from comparative studies of primate cortical organization, highlighting recent findings and hypotheses that may help us to understand the rules governing evolutionary changes of the cortical map and the process of formation of areas during development. We argue that clear unequivocal views of cortical areas and their homologies are more likely to emerge for 'core' fields, including the primary sensory areas, which are specified early in development by precise molecular identification steps. In primates, the middle temporal area is probably one of these primordial cortical fields. Areas that form at progressively later stages of development correspond to progressively more recent evolutionary events, their development being less firmly anchored in molecular specification. The certainty with which areal boundaries can be delimited, and likely homologies can be assigned, becomes increasingly blurred in parallel with this evolutionary/developmental sequence. For example, while current concepts for the definition of cortical areas have been vindicated in allowing a clarification of the organization of the New World monkey 'third tier' visual cortex (the third and dorsomedial areas, V3 and DM), our analyses suggest that more flexible mapping criteria may be needed to unravel the organization of higher-order visual association and polysensory areas.

Accelerated leap methods for simulating discrete stochastic chemical kinetics

Biologists are increasingly conscious of the critical role that noise plays in cellular functions such as genetic regulation, often in connection with fluctuations in small numbers of key regulatory molecules. This has inspired the development of models that capture this fundamentally discrete and stochastic nature of cellular biology - most notably the Gillespie stochastic simulation algorithm (SSA). The SSA simulates a temporally homogeneous, discrete-state, continuous-time Markov process, and of course the corresponding probabilities and numbers of each molecular species must all remain positive. While accurately serving this purpose, the SSA can be computationally inefficient due to very small time stepping so faster approximations such as the Poisson and Binomial τ-leap methods have been suggested. This work places these leap methods in the context of numerical methods for the solution of stochastic differential equations (SDEs) driven by Poisson noise. This allows analogues of Euler-Maruyuma, Milstein and even higher order methods to be developed through the Itô-Taylor expansions as well as similar derivative-free Runge-Kutta approaches. Numerical results demonstrate that these novel methods compare favourably with existing techniques for simulating biochemical reactions by more accurately capturing crucial properties such as the mean and variance than existing methods.

Investigation of the Effect of Array Geometry on the Performance of Free-Space Optical Interconnects

The effect of transmitter and receiver array configurations on the stray-light and diffraction-caused crosstalk in free-space optical interconnects was investigated. The optical system simulation software (Code V) is used to simulate both the stray-light and diffraction-caused crosstalk. Experimentally measured, spectrally-resolved, near-field images of VCSEL higher order modes were used as extended sources in our simulation model. In addition, we have included the electrical and optical noise in our analysis to give more accurate overall performance of the FSOI system. Our results show that by changing the square lattice geometry to a hexagonal configuration, we obtain an overall signal-to-noise ratio improvement of 3 dB. Furthermore, system density is increased by up to 4 channels/mm2.

MQL: A powerful extension to OCL for MOF queries

The Meta-Object Facility (MOF) provides a standardized framework for object-oriented models. An instance of a MOF model contains objects and links whose interfaces are entirely derived from that model. Information contained in these objects can be accessed directly, however, in order to realize the Model-Driven Architecture@trade; (MDA), we must have a mechanism for representing and evaluating structured queries on these instances. The MOF Query Language (MQL) is a language that extends the UML's Object Constraint Language (OCL) to provide more expressive power, such as higher-order queries, parametric polymorphism and argument polymorphism. Not only do these features allow more powerful queries, but they also encourage a greater degree of modularization and re-use, resulting in faster prototyping and facilitating automated integrity analysis. This paper presents an overview of the motivations for developing MQL and also discusses its abstract syntax, presented as a MOF model, and its semantics

Assessing flow in physical activity: The Flow State Scale-2 and Dispositional Flow Scale-2

The Flow State Scale-2 (FSS-2) and Dispositional Flow Scale-2 (DFS-2) are presented as two self-report instruments designed to assess flow experiences in physical activity. Item modifications were made to the original versions of these scales in order to improve the measurement of some of the flow dimensions. Confirmatory factor analyses of an item identification and a cross-validation sample demonstrated a good fit of the new scales. There was support for both a 9-first-order factor model and a higher order model with a global flow factor. The item identification sample yielded mean item loadings on the first-order factor of .78 for the FSS-2 and .77 for the DFS-2. Reliability estimates ranged from .80 to .90 for the FSS-2, and .81 to .90 for the DFS-2. In the cross-validation sample, mean item loadings on the first-order factor were .80 for the FSS-2, and .73 for the DFS-2. Reliability estimates ranged between .80 to .92 for the FSS-2 and .78 to .86 for the DFS-2. The scales are presented as ways of assessing flow experienced within a particular event (FSS-2) or the frequency of flow experiences in chosen physical activity in general (DFS-2).

Activation of visual areas during the attentional blink

When two targets are presented in rapid succession, identification of the first target is nearly perfect while identification of the second is severely impaired at shorter inter-target lags, and then gradually improves as lag increases. This second-target deficit is known as the attentional blink (AB). Numerous studies have implicated competition for access to higher-order processing mechanisms as the primary cause of the AB. However, relatively few studies have directly examined how the AB modulates activity in specific brain areas. To this end, we used fMRI to measure activation in the occipital and parietal cortices (including V1, V2, and area MT) during an AB task. Participants were presented with an initial target of oriented line segments embedded in a central stream of letter distractors. This central target was followed 100 - 700 ms later by a peripheral ‘X’ presented at one of four locations along with three ‘+’ distractors. All peripheral items were presented in the centre of a small field of moving dots. Participants made non-speeded judgments about line-segment orientation and the location of the second target at the end of a trial and to ignore all other stimuli. The results showed a robust AB characterised by a linear improvement in second-target accuracy as lag increased. This pattern of behavioural results was mirrored by changes in activation patterns across a number of visual areas indicating robust modulation of brain activity by the AB.

Direct measurement of pulse distortion near the zero-dispersion wavelength in an optical fiber by frequency-resolved optical gating

The technique of frequency-resolved optical gating is used to characterize the intensity and the phase of picosecond pulses after propagation through 700 m of fiber at close to the zero-dispersion wavelength. Using the frequency-resolved optical gating technique, we directly measure the severe temporal distortion resulting from the interplay between self-phase modulation and higher-order dispersion in this regime. The measured intensity and phase of the pulses after propagation are found to be in good agreement with the predictions of numerical simulations with the nonlinear Schrodinger equation. (C) 1997 Optical Society of America.

Cross-linking studies and membrane localization and assembly of radiolabelled large mechanosensitive ion channel (MscL) of Escherichia coli

The gene encoding the large conductance mechanosensitive ion channel (MscL) of Escherichia coli and several deletion mutants of mscL were cloned under the control of the T7 RNA polymerase promoter. Transformation of these constructs into an E. coli strain carrying an inducible T7 RNA polymerase gene allowed the specific production and labelling of MscL with [S-35]methionine. Preparation of membrane fractions of E. coli cells by sucrose gradient centrifugation indicated that the radiolabelled MscL was present in the inner cytoplasmic membrane in agreement with results of several studies. However, treatment of the labelled cells and cell membrane vesicles with various cross-linkers resulted in the majority of labelled protein migrating as a monomer with a small proportion of molecules (approximate to 25%) migrating as dimers and higher order multimers. This result is in contrast with a finding of a study suggesting that the channel exclusively forms hexamers in the cell membrane off. coli (1) and therefore may have profound implication for the activation and/or ''multimerization'' of the channel by mechanical stress exerted to the membrane. In addition, from the specific activity of the radiolabelled protein and the amount of protein in the cytoplasmic membrane fraction we estimated the number of MscL ion channels expressed under these conditions to be approximately 50 channels per single bacterium. (C) 1997 Academic Press.

Robust algorithms for solving stochastic partial differential equations

A robust semi-implicit central partial difference algorithm for the numerical solution of coupled stochastic parabolic partial differential equations (PDEs) is described. This can be used for calculating correlation functions of systems of interacting stochastic fields. Such field equations can arise in the description of Hamiltonian and open systems in the physics of nonlinear processes, and may include multiplicative noise sources. The algorithm can be used for studying the properties of nonlinear quantum or classical field theories. The general approach is outlined and applied to a specific example, namely the quantum statistical fluctuations of ultra-short optical pulses in chi((2)) parametric waveguides. This example uses a non-diagonal coherent state representation, and correctly predicts the sub-shot noise level spectral fluctuations observed in homodyne detection measurements. It is expected that the methods used wilt be applicable for higher-order correlation functions and other physical problems as well. A stochastic differencing technique for reducing sampling errors is also introduced. This involves solving nonlinear stochastic parabolic PDEs in combination with a reference process, which uses the Wigner representation in the example presented here. A computer implementation on MIMD parallel architectures is discussed. (C) 1997 Academic Press.

Effect of the Bloch-Siegert shift in a strongly driven transition: Asymmetric Autler-Townes profile

Under the conditions of the rotating wave approximation (RWA), a transition strongly driven by a resonant oscillating field displays the well known symmetric Autler-Townes doublet. However, if the counter-rotating component, neglected in the RWA, is taken into account, the Bloch-Siegert shift gives rise to an Autler-Townes doublet of unequal intensity even in the case of a resonant driving field. This effect is investigated theoretically in a V-shaped three-level double-resonance configuration and the results are presented in this paper. An interesting observation is that the level of asymmetry not only depends on the driving-field intensity but also on the characteristics of the driven system including relaxation rates and equilibrium population distributions.

Casimir invariants and characteristic identities for gl(infinity)

A full set of (higher-order) Casimir invariants for the Lie algebra gl(infinity) is constructed and shown to be well defined in the category O-FS generated by the highest weight (unitarizable) irreducible representations with only a finite number of nonzero weight components. Moreover, the eigenvalues of these Casimir invariants are determined explicitly in terms of the highest weight. Characteristic identities satisfied by certain (infinite) matrices with entries from gl(infinity) are also determined and generalize those previously obtained for gl(n) by Bracken and Green [A. J. Bracken and H. S. Green, J. Math. Phys. 12, 2099 (1971); H. S. Green, ibid. 12, 2106 (1971)]. (C) 1997 American Institute of Physics.

Developing logic programs from specifications using stepwise refinement

In this paper we demonstrate a refinement calculus for logic programs, which is a framework for developing logic programs from specifications. The paper is written in a tutorial-style, using a running example to illustrate how the refinement calculus is used to develop logic programs. The paper also presents an overview of some of the advanced features of the calculus, including the introduction of higher-order procedures and the refinement of abstract data types.

Rethinking the development, dissemination and adoption of agricultural technologies

This paper focuses on the higher order factors affecting successful adoption of technologies. Drawing on the "actor-oriented perspective" in rural sociology, it is argued that successful examples of adoption at this higher level result from a complex conjunction of people and events, with outcomes that may have been quite unanticipated at the outset. From this perspective, research and extension projects and programs are viewed as arenas in which social actors–village leaders, farmers, researchers (local and international), aid officials, municipal agents, extension workers, and traders–pursue their own short- and long-term objectives and strategies. To this end, they maneuver, negotiate, organize, cooperate, participate, coerce, obstruct, form coalitions, adopt, adapt, and reject, all within a specific geographical and historical context.